I think the way Bareil died was a bit crummy, and I wish something more grand had happened that would have had harder-hitting consequences for the storyline. I like the suggestion of Winn offing him, perhaps after he helps her with negtiations? Having her cake and eating it to. Just not in the VOY sense.
I do agree with the writers that it was best to have him leave the show, as they had changed their plans with Bajor. Letting him leave the series in a dignified manner is better than keeping him around solely to be Kira's boyfriend. It's a shallow use of a character that was introduced with grander intentions.
I think the Nog storyline was fine though. I understand that the Ferengi as a culture are very annoying, but itsn't that the point here? Jake isn't being understanding of Nog, and is embarressed. Sisko is on the money, and it's his sort of stance that makes DS9 better than TNG at the end of the day.